MultiQC34 SAMtools30 fastp28 BUSCO22 BWA20 Minimap218 gfastats15 BEDTools14 Cutadapt13 FastQC13 Merqury13 Bowtie 212 Bandage10 BCFtools10 BLAST10 Bwa-mem210 kraken29 SRA Software Toolkit9 GenomeScope 2.08 MaBoSS7 MACS7 PhysiCell7 ggplot26 lofreq6 purge_dups6 QUAST6 SCANPY6 QualiMap5 R5 shovill5 snpEff5 Stacks5 StringTie5 taxonomy_krona_chart5 TransDecoder5 antiSMASH4 Cufflinks4 Flye4 Galaxy4 iVar4 Racon4 RepeatMasker4 seqtk4 Seurat4 STAR4 Unicycler4 UniProt4 cisTEM3 gffread3 Gromacs3 HISAT23 Medaka3 MotionCor23 NanoPlot3 Open Babel3 picard_samtofastq3 RDKit3 Scipion3 SPAdes3 ToolDistillator3 Trimmomatic3 Vcflib3 Variant Effect Predictor (VEP)3 AmberTools2 anndata2 Biopython2 BRAKER12 bx-python2 CellProfiler2 ChiRA2 compute_sequence_length2 DESeq22 Diamond2 FASTX-Toolkit2 FreeBayes2 funannotate2 GATK2 HiCExplorer2 Infernal2 Konstanz Information Miner (KNIME)2 nanopolish2 NCBI Datasets2 NGSUtils2 Picard2 PredPrIn2 PretextView2 RepeatModeler2 RSeQC2 Smudgeplots2 SnpSift2 tophat22 VADR2 vardict2 VarScan2 vcfanno2 vcfutils2 VSEARCH2 XMIPP2 YaHS2 ABRicate1 AdapterRemoval1 AGAT1 AnnotSV1 Bakta1 BamTools1 BBMap1 Bioconductor1 Bracken1 CARNIVAL1 cBioPortal1 ChemicalToolbox1 CITE-seq-Count1 Clair31 Clustal 2 (Clustal W, Clustal X)1 Clustal 1.8 (Clustal W, Clustal X)1 clusterProfiler1 CNVkit1 COMBAT-TB Workbench1 cuffdiff1 decoupleR1 Delly21 EGA1 FastTree1 Filtlong1 FLASH1 GADES1 GBMatch - GBMPredictor1 GEMINI1 GSEA1 HiFiAdapterFilt1 Hifiasm1 htseqcount1 HTSlib1 Integron Finder1 iqtree1 ISEScan1 JBrowse 21 KrakenTools1 MAPseq1 Mash1 Matchms1 MaxQuant1 Meryl1 miniasm1 miniprot1 MitoHiFi1 MOB-suite1 MolMeDB1 Metagenomic operational taxonomic units (mOTUs)1 MSMetaEnhancer1 MUMmer1 Newick Utilities1 Nextflow1 nextstrain.org1 ngsReports1 OBITools1 OMArk1 PEAR1 PhysiBoSS1 pilon1 PlasmidFinder1 PLINK1 Prodigal1 progeny1 Proteinortho1 protexcluder1 pyfastaq1 Recentrifuge1 recetox-msfinder1 RepeatModeler1 SeqCode1 SeqSero21 SISTR1 Snakemake1 snippy1 Subread1 SuCOS1 tabix1 TaxonKit1 tb-profiler1 Trim Galore1 UCSC Genome Browser Utilities1 varlociraptor1 WGCNA1 More...

Galaxy302 Nextflow130 Common Workflow Language70 COMPSs58 Snakemake41 Python39 Jupyter28 Docker16 Shell Script13 KNIME8 Workflow Description Language8 Bpipe5 Scipion5 R markdown4 Autosubmit1 BioCompute Object1 Janis1 Perl1 Pi1 Quarto Markdown1 Rbbt1 Uniform Interface to Computing Resources1 More...

Bioinformatics51 covid-1950 PyCOMPSs45 Genomics44 Supercomputer36 Assembly32 data_persistence32 Metagenomics30 Nextflow23 Marenostrum IV22 Transcriptomics21 non_data_persistence20 rna-seq19 Annotation18 CWL18 rna18 COMPSs17 SNPs17 Workflows17 Alignment16 dislib16 ERGA15 Galaxy15 Machine Learning15 workflow15 INDELs14 GATK413 Python13 RNASEQ13 variant calling13 Example12 illumina12 nanopore12 Proteomics12 Tutorial12 variant_calling12 cancer11 image processing11 Marenostrum V11 HiFi10 QC10 imaging9 Large-genome-assembly9 ONT9 covid19.galaxyproject.org8 FASTQ8 Laptop8 SARS-CoV-28 scRNAseq8 Snakemake8 softwareRequirements8 vgp8 Java7 Metabolomics7 scalable7 TSI-annotation7 WGS7 Climate6 DNA6 genome-annotation6 genome_assembly6 Hi-C6 molecular dynamics6 PBS6 single-cell6 Virology6 Virus6 ARTIC5 bacterial-genomics5 bpipe5 BY-COVID5 ChIP5 groovy5 GTN5 mapping5 mass-spectrometry5 NCI5 pediatric5 phylogenetics5 remote_dataset5 SAMTools5 variant-calling5 ABRomics4 antimicrobial resistance4 astronomy4 binning4 Cheminformatics4 ChIP-seq4 Classification4 copernicus4 FAIR workflows4 Gadi4 generic4 genome4 Genome assembly4 Germline4 gpu4 helicase4 HPC4 jupyter4 microbiome4 name:ASSEMBLY+QC4 name:ONT4 NGS4 openms4 rare diseases4 Retrosynthesis4 rna virus4 shotgun4 spa4 10x-genomics3 10xgenomics3 16S3 Amplicon3 AMR3 Assembly+QC3 ATAC-seq3 BUSCO3 BWA3 BWA-mem3 Conversion3 cryoem3 DataQC3 Default-SDR3 denovo-assembly3 Ecology3 eDNA3 EOSC4Cancer3 Epigenomics3 FastQC3 HiC3 hifiasm3 identification3 image-processing3 kallisto3 kraken3 manta3 Merqury3 Metabarcoding3 MetaDEGalaxy3 metatranscriptomics3 mirna prediction3 Multi-omics3 MultiQC3 name:ILLUMINA3 NCI-Gadi3 OME-Zarr3 paired-end3 Pathway Analysis3 pathway prediction3 protein3 quality3 S33 SANBI3 scipion3 scRNA-seq3 Somatic3 STAR3 structural variants3 taxonomic-classification3 taxonomic-profiling3 transcriptome3 18S2 adna2 Alternative splicing2 alternative-splicing2 AMR-detection2 annotsv2 antibiotic-resistance2 antimicrobial-resistance-genes2 bash2 bioimaging2 blast2 BROAD2 CellProfiler2 Cellranger2 CODEX22 collections2 coronavirus2 cosifer2 CTE-Power92 Databases2 Deep learning2 demultiplexing2 dengue2 DE_NOVO2 differential expression2 differential-expression2 DNA-seq2 Earth-system2 Electron microscopy2 ExomeDepth2 exploration2 expression2 fasta2 Flashlite2 GC-MS2 gene set enrichment analysis2 genome-assembly2 Glacios2 GROMACS2 GWAS2 HySEA2 ITS2 iwc2 k-mer2 Knime2 linkage_map2 long-read-sequencing2 long-reads2 MARS-seq2 Matrix Multiplication2 MERS2 Meryl2 metabolic engineering2 microscopy2 mpxv2 MS2 multi-specimen-input2 name:ERGA2 nanopore-sequencing2 NSP132 Ocean2 pangenome2 pangeo2 pathogen2 pathway design2 peak-calling2 personalized medicine2 phylogenomics2 Pipeline2 Profiling2 proteogenomics2 PyTorch2 quality control2 quantification2 Quast2 Report2 Reviewed2 scATAC-seq2 Segmentation2 Semantic Network Analysis2 singularity2 snv2 spatial2 star-solo2 Statistics2 Supernova2 SVD2 synteny2 Synthetic Biology2 TalosArctica2 taxonomy-assignment2 TitanKrios2 Tophat22 TransBioNet2 trinity2 TSI2 Tsunami2 validated-2022-06-292 variant-analysis2 variation2 VARSCAN22 VCF2 WDL2 wes2 west nile2 whole genome sequencing2 workflow4metabolomics2 zika2 #single-cell1 10.3390/microorganisms100202921 10X1 ABR1 abricate1 adaptor1 air-quality1 airr1 alevin1 alphafold21 amp1 amplicon-sequencing1 ampliconarchitect1 ampliconsuite1 ancient-dna1 ancient-dna-analysis1 ancientdna1 antimicrobial-peptides1 arg1 atac1 ATACseq1 automated workflows1 b-cell1 BackTrackBB1 bacteria1 bacterial1 bacterial-genome-analysis1 bacterial-genomes1 BAM1 bamtofastq1 bases2fastq1 BBduk1 bbmap1 bcl2fastq1 Behavioral data1 benchmarking1 bgc1 BGE1 BioBB1 Biodiversity1 bioformats1 bioformats2raw1 BioID1 Bioimage1 Biomedical Ontologies1 BioStudies1 biosynthetic-gene-clusters1 bisulfite-sequencing1 Bootstrapping1 bowtie21 BQSR1 braken1 bustools1 bwa-mem21 C++1 cage1 cage-seq1 cageseq-data1 carveme1 CATH1 causal inference1 cfDNA1 chimeric-alignment1 chromatin-accessibiity1 chromatin-immunoprecipitation1 chromosome-conformation-capture1 CIRCexplorer21 circle-seq1 circrna1 circRNA_finder1 circular1 CIRIquant1 clip1 clip-seq1 cmip61 CNVkit1 common data model1 community-detection1 Community_metrics1 comparative effectiveness1 comparative-genomics1 Compomics1 Consensus1 container1 contamination1 contigs1 coprolite1 Copy Number Variation1 cosmic1 counts1 covid191 cramtofastq1 crispr1 crispr-analysis1 crispr-cas1 cryosparc1 ctat1 cutandrun1 cutandrun-seq1 cutandtag1 cutandtag-seq1 CUTnRUN1 cytometry1 Darwin core1 data annotation1 data fusion1 data integration1 Data package1 data retrieval and transformation1 data transformation1 data wrangling1 data-independent-proteomics1 DataOne1 DCC1 ddbj1 DE1 de novo1 de-identification1 decontamination1 deep-variant1 demo1 denovo1 deseq21 dia1 dia-proteomics1 diagnostics1 DIAMOND1 differential-abundance1 differential_expression1 directed acyclic graph1 disease outcome prediction1 DL1 dna barcoding1 dna-methylation1 Domain-Domain interaction1 dot-plot1 download1 dRNAseq1 dualrna-seq1 durg response simulation1 earth observation1 Earthquake Detection1 eccdna1 ecdna1 Ecological metadata language1 eFlows4HPC1 EGA-archive1 elementbiosciences1 em-seq1 emergen_validated1 EML1 eml-annotation1 ena1 eosc-nordic1 epigenetics1 epigenome1 epitope1 epitope-prediction1 eukaryotes1 evolution1 evolutionary-tree1 Exposomics1 extrachromosomal-circular-dna1 EZyRB1 facs-sorting1 FAIR1 fastp1 fcs1 featurecounts1 file conversion1 filter1 filtering1 find_circ1 fish1 Fragmentomics1 function1 fusion1 fusion-genes1 Galaxy-E1 GATK1 GATK31 GEM1 gene expression correlation1 gene expression data wrangling1 Gene ontology term sets similarity1 Gene Prioritization1 gene-expression1 gene-fusion1 genetic design1 genomic ancestry1 genomics-visualization1 geo1 geo database mining1 ggbio1 GLM1 global assemblies1 gnomad1 gnps1 google1 Gravitational Waves1 GRIDS1 GRIDSS1 gro-seq1 gsea1 GUCFG2galaxy1 GUI1 HaplotyeCaller1 hCNV1 hicar1 high-throughput1 high-throughput_sequencing_analysis1 hla1 hla-typing1 hmdb1 horizontal-gene-transfer1 host-pathogen1 host-pathogen PPIs1 HTSeq1 human1 humann21 Hybrid Workflow1 hybrid-assembly1 image file format1 image-analysis1 image-segmentation1 imageJ1 immcantation1 immunology1 immunorepertoire1 index1 international comparison1 iontorrent1 isoform switching1 isoseq1 isoseq-31 Juicer1 kmeans1 kmer1 kmer-counting1 kmer-frequency-count1 kraken21 Kratos Multiphysics1 krona1 label-free-quantification1 last1 LC-MS1 lfq1 LiftOver1 limma1 linked-reads1 Luigi & Rufus workflow1 macs21 MAG1 Magic1 map1 MapSplice1 Marine omics1 mass-spec1 massbank1 MaxQuant1 memote1 metagenome1 metagenomes1 metaMS1 methyl-seq1 MGE1 mhc1 mhc-binding-prediction1 microarray1 microbial1 minimal-example1 miniTurboID1 MIRACUM1 miRanda1 mlxv1 mnase-seq1 Mobilome1 model1 Modeling1 molecular-pixelation1 molecularcartography1 mpvx1 ms11 ms21 Multivariate1 Mutect21 n501 name:amplicon1 name:PROFILING1 name:single-cell1 nanostring1 nanostringnorm1 nascent1 natural-products1 ncbi sra1 NCI Gadi1 ndvi1 networks1 NGFF1 non-coding1 non-model1 Non-parametric1 nonspliced1 Nord31 NS31 nucleosome1 nucleosome-maps1 nucleosome-positioning1 observation1 OME-TIFF1 openebench1 optitype1 oxford-nanopore1 pacbio1 pairwise-alignment1 parallel1 Parsl1 pathogen-genomics1 pathogenicity score1 Pathology1 Pathway co-occurrence1 pbat1 peptides1 Perl1 Permeability1 personalized-medicine1 Pfam1 phasing1 phylogenetic-placement1 phylogeny1 pixelator1 pixelgen-technologies1 pod51 polygenic risk score1 polygenic score1 population-genetics1 pox1 pre-processing1 prediction1 Presence_absence1 pro-seq1 prokaryotes1 prokka1 Proline1 Protein domains1 protein interactin data triplification1 protein interactions database integration1 protein-databases1 protein-fold-prediction1 protein-folding1 Protein-Protein Interaction1 Protein-Protein interaction prediction1 protein-sequences1 protein-structure1 proteins1 proteins network augmentation1 public cancer datasets exploration1 purge_dups1 pypgatk1 QCxMS1 qiime21 QTL mapping1 quantseq1 radio interferometry1 rare-disease1 rdkit1 readmapping1 reads_selection1 reads_simulation1 Reconstruction1 Reduced Order Modeling1 referencegenome1 Regulatory Mendelian Mutation score1 RELIANCE1 ReMM1 repeat1 repseq1 rice1 rna-rbp-interactions1 rrbs1 rrna1 RSeQC1 salmon1 sambamba1 scientific publication text mining1 screening1 secondary-metabolites1 Segemehl1 Seismic Detection1 Semantic Comparison1 Semantic Interpretation1 sentinel-2 data1 sequence annotation1 sequence search1 sequence-classification1 shiny1 short-reads1 SIM1 single particle analysis1 single-cell-omics1 single-cell-rna-seq1 single-end1 SKA1 slamseq1 small-rna1 smart-seq 21 smoove1 smrna-seq1 SPARK1 spatial-transcriptomics1 Species abundance1 spectra1 splicing1 sra1 st1 strandedness1 StringTie1 structural-variants1 survivor1 SV1 synapse1 synthetic data1 TAD1 tama1 target-panels1 TargetScan1 taxonomies1 taxonomy1 tcga1 TELLSeq1 telomere1 tiddit1 tidyverse1 tmt1 Tomography1 topologically associating domains1 Toxicology1 training1 trajectories1 Trans-Proteomic1 transcription1 transcriptional-dynamics1 tree1 trimming1 tss1 tuberculosis1 tumour1 ultra1 umi1 umis1 Unicycler1 unique-molecular-identifier1 urgent computing1 vaccines1 validaiton o protein interaction predictions1 variant1 variant pathogenicity prediction1 variant-annotation1 viral1 viral-integration1 viruses1 virusintegrationfinder1 visium1 whole-exome-sequencing1 whole-genome-alignment1 whole-genome-sequencing1 wnt signaling1 worflow1 xcms1 More...

WorkflowHub Bot167 Genís Bayarri70 Raül Sirvent30 Anna Syme25 Diego De Panis18 Bert Droesbeke16 Laura Rodriguez-Navas14 Sarah Williams14 Yvan Le Bras11 Ambarish Kumar10 Tracy Chew9 Cristóbal Gallardo9 Anne Fouilloux8 Bart Nijsse8 Jean-Marie Burel8 Miguel Vazquez8 Cristian Tatu8 Fernando Vázquez-Novoa8 Paul De Geest8 Douglas Lowe7 Georgina Samaha7 Yasmmin Martins7 Johan Gustafsson6 Martin Beracochea5 Jasper Koehorst5 Sergi Sayols5 Oliver Woolland5 Tom Brown5 Matthieu Muffato5 Aldar Cabrelles5 Melchior du Lac4 Willem de Koning4 Peter van Heusden4 johan Rollin4 Helena Rasche4 Dennis Dollée4 Konstantinos Kyritsis4 Bryan Raubenolt4 Stian Soiland-Reyes3 Irene Sánchez3 Juma Bayjan3 Mike Thang3 Wolfgang Maier3 Anton Nekrutenko3 Jeanette Reinshagen3 Varsha Kale3 Pablo Riesgo Ferreiro3 Daniel Marchan3 Oliver White3 Timon Schlegel3 Hervé Ménager2 Luca Pireddu2 Robin Long2 Beatriz Serrano-Solano2 Pavankumar Videm2 Ross Thorne2 Sarah Beecroft2 Valentine Murigneux2 Volodymyr Savchenko2 Johannes Köster2 thodk2 Elida Schneltzer2 Pasi Korhonen2 Miguel Roncoroni2 Kary Ocaña2 Cristiane Taniguti2 Peter Menzel2 Adam Tofilski2 Simon Rolph2 David James Sherman2 Tina Tian2 Daan Hazelaar2 Andrea Furlani2 Fabrice Touzain2 Jorge Ejarque2 Rutger Vos2 Nathaniel Matteson2 Kateřina Storchmannová2 Ashish Bhawel2 Xiaolong Luo2 Marie Jossé2 francois moreews1 Camille Juigné1 Laura del Cano1 Ivan Topolsky1 ignacio eguinoa1 Andrea Giachetti1 Michael R. Crusoe1 Matteo Chiara1 Carlos Oscar Sorzano Sanchez1 Paul Brack1 phytopat gembloux1 johan Rollin1 Marco De La Pierre1 Julian Uszkoreit1 Qinqin Long1 Dennis Hendriksen1 Daphne Wijnbergen1 Patrick Durand1 Cyril Noel1 Richard Lupat1 Javier Moldon1 Bianca Pasat1 Rob Edwards1 Valentin Tilloy1 Michael Roach1 Ryan Patterson-Cross1 Alexander Botzki1 Barry Digby1 panou@fleming.gr Panou1 Haris Zafeiropoulos1 Kaur Alasoo1 Hrishikesh Dhondge1 Marvin Martens1 Marlene Rezk1 Naga Kasinadhuni1 Casper de Visser1 Radek Veverka1 Tim Booth1 Samuel Lambert1 Ekaterina Sakharova1 Alejandra Escobar1 Saskia Hiltemann1 bugra oezdemir1 Max Schubach1 Luc Cornet1 Felicita Gernhardt1 Nico Trummer1 Ang Guo1 Diego Garrido-Martín1 Roderic Guigó1 Bruno P. Kinoshita1 Luca Cozzuto1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Stevie Pederson1 Jeffrey Detras1 Thomas Gruber1 Marjan Meurisse1 Vasiliki Panagi1 Khaled Jum'ah1 Jorrit Mesman1 Elisabetta Spinazzola1 Rosa M Badia1 Anand Maurya1 Agata Kilar1 Vincent Hervé1 Markus Konkol1 Jessica Gomez-Garrido1 Akshay Akshay1 Davide Gurnari1 David Yuan1 Daniel Clarke1 Justin Sonneck1 Yi Sun1 Damon-Lee Pointon1 Bram Danneels1 Zafran Hussain Shah1 Denys Savchenko1 Magdalena Antczak1 Michael Hall1 Rafael Terra1 Ziad Al-Bkhetan1 Aishwarya Iyer1 Dominik Lux1 Archit Dabral1 Andrii Neronov1 Michael Lloyd1 Arnau Soler Costa1 Thomas Roetzer-Pejrimovsky1 Helge Hecht1 Kristina Gomoryova1 Wudmir Rojas1 Carlos Classen1 Usman Rashid1 dan rick1 Pavel Akhtyamov1 Francesco Messina1 Sebastian Röner1 Ann-Kathrin Dörr1 仕卓 张1 Mahesh Binzer-Panchal1 Michael Lynch1 Jen-Hung Wang1 More...

BioBB Building Blocks80 nf-core72 Intergalactic Workflow Commission (IWC)63 Australian BioCommons45 Workflows and Distributed Computing36 iwc33 Galaxy Australia30 ERGA Assembly22 GalaxyProject SARS-CoV-221 usegalaxy-eu19 QCIF Bioinformatics18 Sydney Informatics Hub16 UNLOCK13 COMPSs Tutorials12 PNDB11 EuroScienceGateway11 eFlows4HPC general11 Galaxy Training Network10 MGnify9 Galaxy Climate8 OME8 PerMedCoE8 IBISBA Workflows7 HoloFood at MGnify7 yPublish - Bioinfo tools7 CWL workflow SARS-CoV-26 Integrated and Urban Plant Pathology Laboratory6 EGA6 IMBforge5 UX trial team5 iPC: individualizedPaediatricCure5 EJPRD WP13 case-studies workflows5 Specimen Data Refinery5 Cluster Emergent del Cervell Humà5 Biodiversity Genomics Europe (general)5 NanoGalaxy4 Seq4AMR4 SANBI Pathogen Bioinformatics4 Biodata Analysis Group4 Tree of Life Genome Analysis4 Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases4 SARS-CoV-2 Data Hubs3 ODA3 CO2MICS Lab3 EU-Openscreen3 TRON gGmbH3 Euro-BioImaging3 ERGA Annotation3 Scipion CNB3 BY-COVID (general)3 NHM Clark group3 nf-core viralrecon2 V-Pipe2 EOSC-Life - Demonstrator 7: Rare Diseases2 Pawsey Supercomputing Research Centre2 SeBiMER2 Snakemake-Workflows2 Applied Computational Biology at IEG/HMGU2 INFRAFRONTIER workflows2 TransBioNet2 CRC Cohort2 Workflows Australia2 Medizinisches Proteom-Center, Medical Bioinformatics2 usegalaxy.be workflows2 Air Quality Prediction2 Read2Map2 ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression2 KircherLab2 Apis-wings2 TRE-FX2 BioDT Use Case 4.1.1.2 Ecosystem services2 MISTIC2 Workflows for geographic science2 Katdetectr2 ANSES-Ploufragan2 Pillar III: Urgent computing for natural hazards2 Tree of Life Genome Assembly2 CholGen2 Chemical Data Lab2 Peter Menzel's Team2 Genome Data Compression Team2 RECETOX SpecDatRI2 FAIR-EASE2 NMR Workflow1 COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource1 Italy-Covid-data-Portal1 EOSC-Life-WP6-Demos1 EOSC-Life WP31 MOLGENIS1 Janis1 IAA-CSIC1 FAME1 CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus1 HecatombDevelopment1 OpenEBench1 Bioinformatics and Biostatistics (BIO2 ) Core1 VIB Bioinformatics Core1 Single Cell Unit1 emo-bon1 CINECA1 Toxicology community1 Gyn Department1 AGRF BIO1 X-omics1 CAPSID1 Edinburgh Genomics1 NBIS1 BCCM_ULC1 Computational Science at HZDR1 Big data in biomedicine1 Guigó lab1 Statistical genetics1 Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation1 Bioinformatics Unit @ CRG1 BSC-CES1 ELIXIR Proteomics1 Black Ochre Data Labs1 IRRI Bioinformatics Group1 Zavolan Lab1 Metabolomics-Reproducibility1 NGFF Tools1 Bioinformatics workflows for life science1 Helmholtz Scientific Project Workflow Platform1 BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection1 Lake Erken modelling setup1 EOSC-Life WP3 OC Team, cross RI project1 ARA-dev1 Mendel Centre for Plant Genomics and Proteomics1 Metagenomic tools1 Pillar I: Manufacturing1 Polygenic Score Catalog1 MLme: Machine Learning Made Easy1 Dioscuri TDA1 NIH CFDE Playbook Workflow Partnership1 MMV-Lab1 EMBL-CBA1 EBP-Nor1 Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data1 Bioinformatics Laboratory for Genomics and Biodiversity (LBGB)1 Pangenome database project1 HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment1 Building spatio-temporal workflows in Galaxy1 CEMCOF1 Jackson Laboratory NGS-Ops1 BRAIN - Biomedical Research on Adult Intracranial Neoplasms1 Proteomics CEITEC1 Institute for Human Genetics and Genomic Medicine Aachen1 Plant-Food-Research-Open1 WGGC1 ELIXIR Metabolomics1 Medvedeva Lab1 16S rRNA Analysis1 Protein-protein and protein-nucleic acid binding site prediction research1 Culhane Lab1 IDUN - Drug Delivery and Sensing1 More...

Independent Teams254 BioExcel80 nf-core72 Australian BioCommons72 eFlows4HPC52 COVID-19 Biohackathon31 ERGA25 ELIXIR15 Galaxy10 HoloFood7 Sanger Tree of Life6 DISSCo - Distributed System of Scientific Collections5 Biodiversity Genomics Europe (BGE)5 EOSC-Life3 ELIXIR Belgium2 BioDT2 GenomeDataCompression2 EIRENE-CZ2 EOSC-Life-WP61 BeYond-COVID (BY-COVID)1 JKU 1 IRRI-Bioinformatics1 HELIPORT1 Coupled Catchment Lake Modelling1 AquaINFRA1 Proteomics CEITEC1 WGGC1 IKIM 16S Analysis1 More...

Adam Hospital76 Genís Bayarri75 Anna Syme24 Diego De Panis18 Bart Nijsse13 Tracy Chew13 Jasper Koehorst12 Yvan Le Bras10 Georgina Samaha10 Laura Rodriguez-Navas9 Rosemarie Sadsad9 Martin Beracochea8 Jean-Marie Burel8 Cristian Tatu8 Delphine Lariviere7 Saskia Hiltemann7 Javier Conejero7 Douglas Lowe6 José Mª Fernández6 Raül Sirvent6 Coline Royaux5 Sergi Sayols5 Aldar Cabrelles5 Melchior du Lac4 Friederike Ehrhart4 Gareth Price4 Oliver Woolland4 Cali Willet4 Pierre Marin4 Jorge Ejarque4 Bryan Raubenolt4 Ambarish Kumar3 Juma Bayjan3 Ozan Ozisik3 Patrick Durand3 Laura Leroi3 Laurence Livermore3 Germán Royval3 Cristóbal Gallardo3 Cenna Doornbos3 Jeanette Reinshagen3 Ekaterina Sakharova3 Tom Brown3 Konstantinos Kyritsis3 Clea Siguret3 Ivan Topolsky2 Luca Pireddu2 Anne Fouilloux2 Michael R. Crusoe2 Pavankumar Videm2 Wolfgang Maier2 Julian Uszkoreit2 Valentine Murigneux2 Alexandre Cormier2 Cyril Noel2 Pierre Cuzin2 Mike Thang2 Volodymyr Savchenko2 Philipp Gormanns2 Kary Ocaña2 Varsha Kale2 Tatiana Gurbich2 Cristiane Taniguti2 Peter Menzel2 Diego Garrido-Martín2 Roderic Guigó2 Andrea Furlani2 Denys Savchenko2 Ziad Al-Bkhetan2 Helge Hecht2 Zargham Ahmad2 Stian Soiland-Reyes1 Camille Juigné1 Willem de Koning1 Pau Andrio1 Johan Gustafsson1 Matthias Haimel1 Carlos Oscar Sorzano Sanchez1 Paul Brack1 Sarah Beecroft1 Marco De La Pierre1 Helena Rasche1 Richard Lupat1 Johannes Köster1 Valentin Tilloy1 Michael Roach1 Elida Schneltzer1 Luiz Gadelha1 Asier Gonzalez-Uriarte1 Wolfgang Maier1 Woosub Shin1 Ryan Patterson-Cross1 Anthony Bretaudeau1 Barry Digby1 Haris Zafeiropoulos1 Hrishikesh Dhondge1 Kim Philipp Jablonski1 Pasi Korhonen1 Marvin Martens1 Tazro Inutano1 Marlene Rezk1 Casper de Visser1 Jasper Ouwerkerk1 Benjamin Wingfield1 Anna Niehues1 Marie-Dominique Devignes1 Tim Booth1 Samuel Lambert1 Alejandra Escobar1 Katherine Farquharson1 Lucas Cruz1 Pablo Riesgo Ferreiro1 Felicita Gernhardt1 Andrey Prjibelski1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Stevie Pederson1 Veit Schwämmle1 Anton Korobeynikov1 Luiz Gadelha1 Vasiliki Panagi1 Jorrit Mesman1 Elisabetta Spinazzola1 Rosa M Badia1 Agata Kilar1 Jessica Gomez-Garrido1 Sagane Joye-Dind1 Akshay Akshay1 Phuong Doan1 Davide Gurnari1 David Yuan1 Justin Sonneck1 Damon-Lee Pointon1 William Eagles1 Zafran Hussain Shah1 Kateřina Storchmannová1 Fernando Vázquez-Novoa1 Nandan Deshpande1 Michael Hall1 Rafael Terra1 Ian Brennan1 Aishwarya Iyer1 Dominik Lux1 Ashish Bhawel1 Andrii Neronov1 Amy Curwin1 Arnau Soler Costa1 Thomas Roetzer-Pejrimovsky1 Xiaolong Luo1 Kristina Gomoryova1 Elliott J. Price1 Wudmir Rojas1 Carlos Classen1 Jordi Rambla1 Timon Schlegel1 Pavel Akhtyamov1 Francesco Messina1 Sebastian Röner1 Ann-Kathrin Dörr1 Marie Jossé1 仕卓 张1 Mahesh Binzer-Panchal1 Martin Pippel1 Jen-Hung Wang1 More...

BioCommons ‘Bring Your Own Data’ Expansion Project39 Interactive Jupyter Notebooks for FAIR and reproducible biomolecular simulation workflows17 Tutorials for BioExcel Building Blocks (BioBB)11 Workflows in EuroScienceGateway10 scRNAseq processing in galaxy8 COMPSs Workflows from 2024 Tutorial8 TSI annotation workflows7 Freely accessible ready to use global infrastructure and workflows for SARS-CoV-2 monitoring6 IDR6 ERGA Assembly Galaxy HiFi & HiC Pipelines (Hifiasm-HiC + Purge_Dups + YaHS)6 16S Microbial Analysis with mothur (on Galaxy Australia)6 ERGA Assembly Galaxy ONT+Illumina & HiC Pipelines (NextDenovo-HyPo + Purge_Dups + YaHS)6 ERGA Assembly Galaxy ONT+Illumina & HiC Pipelines (Flye-HyPo + Purge_Dups + YaHS)6 ERGA Assembly Galaxy HiFi & HiC Pipelines (Hifiasm-solo + Purge_Dups + YaHS)6 BioExcel Building Blocks (BioBB) Protein MD Setup Tutorials5 EuCanImage FHIR ETL Implementation5 HiFi genome assembly on Galaxy4 Vertebrate Genomes Pipelines (VGP) workflows3 CEITEC CryoEM Facility Workflows3 BY-COVID related workflows3 ERGA Assembly Snakemake HiFi & HiC Pipelines3 Genome Evaluation for ERGA-BGE Reports3 TronFlow2 Genome Assembly Workflows for ERGA-BGE genomes2 Sanger Tree of Life Assembly method1 More...

Bioinformatics29 Whole genome sequencing26 Sequence assembly22 Genetic variation18 Genomics16 Transcriptomics15 Metagenomics12 Biomedical science11 Computer science10 Population genomics9 Biodiversity8 Ecology8 Gene expression8 Sequence analysis6 Biological databases5 Data mining5 Metagenomic sequencing5 Oncology5 Compound libraries and screening4 Gene transcripts4 Sequencing4 Workflows4 Bioimaging3 Data quality management3 DNA mutation3 DNA polymorphism3 Drug discovery3 Imaging3 Machine learning3 Preclinical and clinical studies3 Protein interactions3 Sample collections3 Virology3 Copy number variation2 Data integration and warehousing2 Data visualisation2 Exome sequencing2 Gene structure2 Genetics2 Infectious disease2 Microbiology2 Molecular interactions, pathways and networks2 Protein interaction experiment2 Proteomics2 Quantitative genetics2 Rare diseases2 Structural variation2 Cell biology1 Cheminformatics1 ChIP-seq1 Computational biology1 Computational chemistry1 Data submission, annotation and curation1 DNA packaging1 Environmental science1 Epigenomics1 Human genetics1 Mapping1 Marine biology1 Medical imaging1 Medical informatics1 Metabolomics1 Metatranscriptomics1 Microbial ecology1 Molecular genetics1 Nucleic acid sites, features and motifs1 Ontology and terminology1 Pathology1 Pharmacology1 Phylogenetics1 Phylogenomics1 Physics1 Protein binding sites1 Protein folds and structural domains1 Protein variants1 Public health and epidemiology1 Small molecules1 Structural genomics1 Systems biology1 More...

Genome assembly17 Sequencing quality control16 Variant calling12 Expression analysis7 Sequence assembly7 Variant filtering7 Sequence clustering6 Sequence alignment5 Taxonomic classification5 Annotation4 De-novo assembly4 Conversion3 Data retrieval3 Gene-set enrichment analysis3 Haplotype mapping3 Protein interaction network analysis3 Sequence assembly validation3 Transcriptome assembly3 Variant classification3 Calculation2 Copy number variation detection2 Correlation2 Differential gene expression profiling2 Genetic mapping2 Indel detection2 Modelling and simulation2 Prediction and recognition2 Protein interaction network prediction2 Scaffolding2 Sequence assembly visualisation2 SNP annotation2 SNP detection2 Weighted correlation network analysis2 Analysis1 Antimicrobial resistance prediction1 Binding site prediction1 Classification1 Clustering1 Contact map calculation1 Data handling1 Differential protein expression profiling1 Dimensionality reduction1 DNA barcoding1 Enrichment analysis1 Expression correlation analysis1 Feature extraction1 Filtering1 Format detection1 Gene expression profiling1 Gene functional annotation1 Genome alignment1 Genome analysis1 Genome annotation1 Genome comparison1 Genome visualisation1 ID mapping1 Image analysis1 Information retrieval1 k-mer counting1 Mapping1 Metabolic pathway prediction1 Named-entity and concept recognition1 Network analysis1 Nucleic acid property calculation1 Operation1 Peptide identification1 Phasing1 Protein identification1 Protein-protein interaction analysis1 Read mapping1 Relation extraction1 RNA-Seq analysis1 Sequence alignment analysis (site correlation)1 Sequence contamination filtering1 Sequence cutting1 Sequence distance matrix generation1 Sequence profile generation1 Sequence trimming1 Single particle analysis1 Standardisation and normalisation1 Text annotation1 Text mining1 Transcription factor binding site prediction1 Validation1 Visualisation1 More...

Stable323 Work-in-progress94 Deprecated6

Passing74 Not available11 All failing5